RP44A_ARATH
ID RP44A_ARATH Reviewed; 933 AA.
AC Q9SHL7; Q93ZK2;
DT 20-JAN-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Exosome complex exonuclease RRP44 homolog A {ECO:0000305};
DE Short=RRP44 homolog A {ECO:0000305};
DE EC=3.1.13.-;
DE EC=3.1.26.-;
DE AltName: Full=Protein EMBRYO DEFECTIVE 2763 {ECO:0000305};
DE AltName: Full=Ribosomal RNA-processing protein 44A {ECO:0000305};
DE Short=AtRRP44A {ECO:0000303|PubMed:24244451};
GN Name=RRP44A {ECO:0000303|PubMed:24244451};
GN Synonyms=EMB2763 {ECO:0000312|EMBL:AEC06638.1};
GN OrderedLocusNames=At2g17510 {ECO:0000312|Araport:AT2G17510};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=20798041; DOI=10.1073/pnas.1007060107;
RA Zhang W., Murphy C., Sieburth L.E.;
RT "Conserved RNaseII domain protein functions in cytoplasmic mRNA decay and
RT suppresses Arabidopsis decapping mutant phenotypes.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:15981-15985(2010).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=24244451; DOI=10.1371/journal.pone.0079219;
RA Kumakura N., Otsuki H., Tsuzuki M., Takeda A., Watanabe Y.;
RT "Arabidopsis AtRRP44A is the functional homolog of Rrp44/Dis3, an exosome
RT component, is essential for viability and is required for RNA processing
RT and degradation.";
RL PLoS ONE 8:E79219-E79219(2013).
CC -!- FUNCTION: Catalytic component of the RNA exosome complex which has
CC 3'->5' exoribonuclease activity and participates in a multitude of
CC cellular RNA processing and degradation events. Required for 5.8S rRNA
CC intermediate processing and the degradation of 5' external transcribed
CC spacer (5' ETS), a maturation by-product of rRNA synthesis. Is not
CC involved in the degradation of turnip crinkle virus (TCV) RNA and
CC significant virus resistance (PubMed:24244451). Required for normal
CC development of female gametophytes and early embryogenesis
CC (PubMed:20798041, PubMed:24244451). {ECO:0000269|PubMed:20798041,
CC ECO:0000269|PubMed:24244451}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q08162};
CC -!- SUBUNIT: Probable component of the RNA exosome complex.
CC {ECO:0000250|UniProtKB:Q08162}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20798041}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences. {ECO:0000305};
CC Name=1;
CC IsoId=Q9SHL7-1; Sequence=Displayed;
CC -!- DISRUPTION PHENOTYPE: Aborted development of female gametophytes.
CC {ECO:0000269|PubMed:20798041, ECO:0000269|PubMed:24244451}.
CC -!- SIMILARITY: Belongs to the RNR ribonuclease family. {ECO:0000305}.
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DR EMBL; AC007584; AAD32908.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC06638.1; -; Genomic_DNA.
DR EMBL; AY057479; AAL09713.1; -; mRNA.
DR EMBL; AY090298; AAL90959.1; -; mRNA.
DR PIR; A84553; A84553.
DR RefSeq; NP_565418.1; NM_127305.3. [Q9SHL7-1]
DR AlphaFoldDB; Q9SHL7; -.
DR SMR; Q9SHL7; -.
DR STRING; 3702.AT2G17510.2; -.
DR iPTMnet; Q9SHL7; -.
DR PaxDb; Q9SHL7; -.
DR PRIDE; Q9SHL7; -.
DR ProteomicsDB; 228229; -. [Q9SHL7-1]
DR EnsemblPlants; AT2G17510.1; AT2G17510.1; AT2G17510. [Q9SHL7-1]
DR GeneID; 816257; -.
DR Gramene; AT2G17510.1; AT2G17510.1; AT2G17510. [Q9SHL7-1]
DR KEGG; ath:AT2G17510; -.
DR Araport; AT2G17510; -.
DR eggNOG; KOG2102; Eukaryota.
DR HOGENOM; CLU_002333_5_0_1; -.
DR OMA; VVKRNWR; -.
DR PhylomeDB; Q9SHL7; -.
DR PRO; PR:Q9SHL7; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9SHL7; baseline and differential.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000178; C:exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
DR GO; GO:0004519; F:endonuclease activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR041505; Dis3_CSD2.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR002716; PIN_dom.
DR InterPro; IPR001900; RNase_II/R.
DR InterPro; IPR022966; RNase_II/R_CS.
DR InterPro; IPR033771; Rrp44_CSD1.
DR InterPro; IPR033770; RRP44_S1.
DR Pfam; PF17849; OB_Dis3; 1.
DR Pfam; PF13638; PIN_4; 1.
DR Pfam; PF00773; RNB; 1.
DR Pfam; PF17216; Rrp44_CSD1; 1.
DR Pfam; PF17215; Rrp44_S1; 1.
DR SMART; SM00670; PINc; 1.
DR SMART; SM00955; RNB; 1.
DR SUPFAM; SSF50249; SSF50249; 3.
DR SUPFAM; SSF88723; SSF88723; 1.
DR PROSITE; PS01175; RIBONUCLEASE_II; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Endonuclease; Exonuclease; Exosome; Hydrolase;
KW Magnesium; Metal-binding; Nuclease; Nucleus; Reference proteome;
KW RNA-binding; rRNA processing.
FT CHAIN 1..933
FT /note="Exosome complex exonuclease RRP44 homolog A"
FT /id="PRO_0000435321"
FT DOMAIN 50..163
FT /note="PINc"
FT /evidence="ECO:0000255"
FT REGION 296..336
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 481
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q08162"
FT BINDING 490
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q08162"
SQ SEQUENCE 933 AA; 104996 MW; B2A38DB8BEF3DCE3 CRC64;
MLQSKVFNKK TRGGRIQKQV REVYLRDDIY CGAFSCKSCD SSAARLSSSK IIVVDTNVVL
HQIDLLENKA IDTVVVLSVV LDEVKNRNRS VYNRIRLLCS NPARQFYVFS NHVHKDTYVQ
AMEKESANDH NDRAIRVATL WYQKHLGDTS QVLLVTNDRE NKRKATEEGI SAETIEAYVK
SLGQPELLDL LAQPTNEDIT MEDADDSRPS KRKLIYQEHK PMSEITAGLH RGIYHQGKLR
VNRFNPYEAY VGSESIGEEI IIYGRSNMNR AFDGDIVAVE LLPRDQWQDE KALSIAEEDD
EEDDTVHLAP DNVDDAPRTS NLSHETSGDK NAAPVRPSGR VVGVIRRNWH SYCGSLEPMS
LPAGSGGTAH ALFVSKDRRI PKIRINTRQL QNLLDMRIVV AVDSWDRQSR YPSGHYVRPI
GKIGDKETET EVVLIENDVD YSPFSSQVLA CLPPLPWSVS SEDVSNPVRQ DLRHLLVFSV
DPPGCKDIDD ALHCTSLPNG NFELGVHIAD VTNFVHPGTP LDDEASKRGT SVYLVERRID
MLPKPLTEDI CSLRADVERL AFSVIWEMSP DAEIISTRFT KSIIKSSAAL SYIEAQARMD
DSRLTDSLTT DLRNMNTLAK IMRQRRIDRG ALTLASAEVK FDIDPENHDP LNIGMYQILE
ANQMVEEFML AANVSVAGQI LKLFPSCSLL RRHPTPTREM LEPLLRTAAA IGLTLDVSSS
KALADSLDRA VGEDPYFNKL IRILATRCMT QAVYFCSGDL SPPEYHHYGL AAPLYTHFTS
PIRRYADVFV HRLLAASLGI YKLPTVFQDR PQLTSVADNL NYRHRNAQMA GRASVELYVL
IYFRTRPTDE EARVVKIRSN GFIVFVPKYG IEGPVYLTGK GEKGAGDWYV DEEKQKIVKM
DGSLSYSVLQ TVKIHMEVVE PQPNRPKLQL TLL
